Analyze substrate solvation¶

This notebook demonstrates deposition of an SDS adsorption layer on a non-spherical AFM tip model.

Initialization¶

IPython magic¶

%load_ext autoreload
%autoreload 2

%aimport

Modules to reload:
all-except-skipped

Modules to skip:

Imports¶

import ase.io # here used for reading pdb files
from ase.visualize import view
from ase.visualize.plot import plot_atoms # has nasty offset issues
from cycler import cycler # here used for cycling through colors in plots
import datetime
import fabric # for pythonic ssh connections
from fireworks import LaunchPad, Firework, Tracker, Workflow 
from fireworks import FileTransferTask, PyTask, ScriptTask

# FireWorks functionality 
from fireworks import Firework, LaunchPad, ScriptTask, Workflow
from fireworks.user_objects.firetasks.templatewriter_task import TemplateWriterTask
from fireworks.user_objects.firetasks.filepad_tasks import AddFilesTask, GetFilesTask, GetFilesByQueryTask
from imteksimfw.fireworks.user_objects.firetasks.cmd_tasks import CmdTask
from fireworks.utilities.filepad import FilePad # direct FilePad access, similar to the familiar LaunchPad

from collections.abc import Iterable
import glob
import gc # manually clean up memory with gc.collect()
import gromacs # GromacsWrapper, here used for evoking gmc commands, reading and writing .ndx files
# from io import StringIO, TextIOWrapper
import io
from IPython.display import display, Image #, Video # display image files within notebook
from ipywidgets import Video  # display video within notebook
import itertools # for products of iterables
import json # generic serialization of lists and dicts
import jinja2 # here used for filling packmol input script template
import jinja2.meta # for gathering variables in a jinja2 template
import logging 
import matplotlib.pyplot as plt
import MDAnalysis as mda # here used for reading and analyzing gromacs trajectories
import MDAnalysis.analysis.rdf as mda_rdf
import MDAnalysis.analysis.rms as mda_rms
from mpl_toolkits.mplot3d import Axes3D # here used for 3d point cloud scatter plot
import miniball # finds minimum bounding sphere of a point set
import nglview
import numpy as np
import os, os.path
import pandas as pd
import panedr # reads GROMACS edr into pandas df, requires pandas and pbr
import parmed as pmd # has quite a few advantages over ASE when it comes to parsing pdb
from pprint import pprint
import pymongo # for sorting in queries
import scipy.constants as sc
import subprocess # used for evoking external packmol
import sys
import tempfile
import yaml

NOTE: Some configuration directories are not set up yet: 
	/home/centos/.gromacswrapper
	/home/centos/.gromacswrapper/qscripts
	/home/centos/.gromacswrapper/templates
NOTE: You can create the configuration file and directories with:
	>>> import gromacs
	>>> gromacs.config.setup()

GromacsWrapper might need a file ~/.gromacswrapper.cfg with content

[Gromacs]
tools = gmx gmx_d 
# gmx_mpi_d gmx_mpi_d

# name of the logfile that is written to the current directory
logfilename = gromacs.log

# loglevels (see Python's logging module for details)
#   ERROR   only fatal errors
#   WARN    only warnings
#   INFO    interesting messages
#   DEBUG   everything

# console messages written to screen
loglevel_console = INFO

# file messages written to logfilename
loglevel_file = DEBUG

in order to know the GROMACS executables it is allowed to use. Otherwise, calls to gmx_mpi or gmx_mpi_d without MPI wrapper might lead to MPI warnings in output that cause GromacsWrapper to fail.

Logging¶

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger()
logger.setLevel(logging.INFO)

ParmEd needs to know the GROMACS topology folder, usually get this from envionment variable GMXLIB:

Function definitions¶

def find_undeclared_variables(infile):
    """identify all variables evaluated in a jinja 2 template file"""
    env = jinja2.Environment()
    with open(infile) as template_file:
        parsed = env.parse(template_file.read())

    undefined = jinja2.meta.find_undeclared_variables(parsed)
    return undefined

def memuse():
    """Quick overview on memory usage of objects in Jupyter notebook"""
    # https://stackoverflow.com/questions/40993626/list-memory-usage-in-ipython-and-jupyter
    # These are the usual ipython objects, including this one you are creating
    ipython_vars = ['In', 'Out', 'exit', 'quit', 'get_ipython', 'ipython_vars']

    # Get a sorted list of the objects and their sizes
    return sorted([(x, sys.getsizeof(globals().get(x))) for x in dir(sys.modules['__main__']) if not x.startswith('_') and x not in sys.modules and x not in ipython_vars], key=lambda x: x[1], reverse=True)

Global settings¶

# pandas settings
pd.options.display.max_rows = 200
pd.options.display.max_columns = 16
pd.options.display.max_colwidth = 256

os.environ['GMXLIB'] = '/gmx_top'

# pmd.gromacs.GROMACS_TOPDIR = os.environ['GMXLIB']
pmd.gromacs.GROMACS_TOPDIR = '/gmx_top'

# prefix = '/mnt/dat/work/testuser/indenter/sandbox/20191110_packmol'
prefix = '/mnt/dat/work'

work_prefix = '/mnt/dat/work/tmp'

try:
    os.mkdir(work_prefix)
except FileExistsError as exc:
    print(exc)

[Errno 17] File exists: '/mnt/dat/work/tmp'

os.chdir(work_prefix)

# the FireWorks LaunchPad
lp = LaunchPad.auto_load() #Define the server and database
# FilePad behaves analogous to LaunchPad
fp = FilePad.auto_load()

Conversion from LAMMPS data format to PDB¶

The following bash / tcl snippet converts a LAMMPS data file to PDB, assigning the desired names as mapped in a yaml file

#!/bin/bash
# echo "package require jlhvmd; jlh lmp2pdb indenter.lammps indenter.pdb" | vmd -eofexit
vmd -eofexit << 'EOF'
package require jlhvmd
topo readlammpsdata indenter.lammps
jlh type2name SDS_type2name.yaml
jlh name2res  SDS_name2res.yaml
set sel [atomselect top all]
$sel writepdb indenter.pdb
EOF

pdb_chain.py indenter.pdb > indenter_wo_chainid.pdb
pdb_reres_by_atom_9999.py indenter_wo_chainid.pdb > indenter_reres.pdb

Requires

VMD (tested with 1.9.3) with topotools
jlhvmd VMD plugin: https://github.com/jotelha/jlhvmd
pdb-tools: https://github.com/haddocking/pdb-tools/

Overview¶

Overview on projects in database¶

query = {'metadata.datetime': {'$gt': '2020'} }

fp.filepad.count_documents(query)

11975

aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 'project': '$metadata.project' },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # pull 'project' field up in hierarchy
        "$addFields": { 
            "project": "$_id.project",
        },
    },
    {  # drop nested '_id.project'
        "$project": { 
            "_id": False 
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

# sort_aggregation
#aggregation_pipeline = [ match_aggregation, group_aggregation, set_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [c for c in cursor]
res_df = pd.DataFrame(data=res) # pandas Dataframe is just nice for printing in notebook

res_df

Overview on steps in project¶

project_id = '2020-10-13-ctab-on-au-111-substrate-passivation'

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

2824

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['step', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

res_df['step'].values

array(['SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:PDBCleanup:push_filepad',
       'SubstratePassivation:CylindricalPackingAndEquilibartion:CylindricalPacking:CylindricalPackingMain:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:PDBCleanup:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_filepad',
       'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad',
       'SubstratePassivation:ComponentMeasures:SubstratePreparation:FormatConversion:push_filepad',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsTrajectoryVisualization:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:GromacsNPTEquilibrationMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:GromacsPrepMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsEnergyMinimizationAfterSolvationMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:GromacsRelaxationMain:push_infiles',
       'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:SurfactantMoleculeMeasuresMain:push_infiles',
       'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:GromacsNVTEquilibrationMain:push_infiles'],
      dtype=object)

Overview on objects in project¶

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

2824

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'step', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Overview on images by distinct steps¶

query = {
    'metadata.project': project_id,
    'metadata.type': 'png_file',
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

1

# check files degenerate by 'metadata.type' ad 'metadata.name'

aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
                'step': '$metadata.step',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['step', 'type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

res_df["step"][0]

'SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad'

Packing visualization¶

Surfactant measures¶

query = {
    'metadata.project': project_id,
    'metadata.type': 'png_file',
    'metadata.step': {'$regex': 'SurfactantMoleculeMeasures'}
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

1

# check files degenerate by 'metadata.type' ad 'metadata.name'

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["gfs_id"])
    with tempfile.NamedTemporaryFile(suffix='.png') as tmp:
        tmp.write(content)
        obj_list.append(Image(filename=tmp.name)) 
    print('.',end='')

.

obj_list[0]

Energy minimization after solvation analysis¶

Overview on objects in step¶

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'}
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

947

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Global observables¶

query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'},
    "metadata.type": 'energy_file',
}
fp.filepad.count_documents(query)

46

#parameter_dict = {'nmolecules': 'metadata.system.surfactant.nmolecules'}
#parameter_dict = {'shape': 'metadata.system.surfactant.aggregates.shape'}
parameter_dict = {
    'nmolecules': 'metadata.system.surfactant.nmolecules',
    'shape': 'metadata.system.surfactant.aggregates.shape'
}

parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res_mi_list = []

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        try:
            em_df = panedr.edr_to_df(tmp.name)
        except:
            logger.warning("Failed reading edr for {}".format(metadata))
            continue
        
        mi = pd.MultiIndex.from_product(
            [c["_id"].values(),em_df.index],
            names=[*c["_id"].keys(),'step'])
        em_mi_df = em_df.set_index(mi)        
        res_mi_list.append(em_mi_df)
    print('.',end='')
print('')

res_mi_df = pd.concat(res_mi_list)
res_df = res_mi_df.reset_index()

WARNING:root:Failed reading edr for {'_id': ObjectId('5f8673106b7f8f8ab3bb6dd7'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-07-777197/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-07-777197/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.970518', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on Au(111) substrate passivation', 'owners': [{'name': 'Johannes Laurin Hörmann', 'email': 'johannes.hoermann@imtek.uni-freiburg.de', 'username': 'fr_jh1130', 'orcid': '0000-0001-5867-695X'}], 'machine': 'juwels', 'mode': 'production', 'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules', 'm': 'system->counterion->nmolecules', 's': 'system->surfactant->aggregates->shape'}, 'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'}, {'n': 81, 'm': 81, 's': 'cylinders'}, {'n': 162, 'm': 162, 's': 'bilayer'}, {'n': 162, 'm': 162, 's': 'cylinders'}, {'n': 243, 'm': 243, 's': 'bilayer'}, {'n': 243, 'm': 243, 's': 'cylinders'}, {'n': 324, 'm': 324, 's': 'bilayer'}, {'n': 324, 'm': 324, 's': 'cylinders'}, {'n': 405, 'm': 405, 's': 'bilayer'}, {'n': 405, 'm': 405, 's': 'cylinders'}, {'n': 486, 'm': 486, 's': 'bilayer'}, {'n': 486, 'm': 486, 's': 'cylinders'}, {'n': 567, 'm': 567, 's': 'bilayer'}, {'n': 567, 'm': 567, 's': 'cylinders'}, {'n': 648, 'm': 648, 's': 'bilayer'}, {'n': 648, 'm': 648, 's': 'cylinders'}, {'n': 729, 'm': 729, 's': 'bilayer'}, {'n': 729, 'm': 729, 's': 'cylinders'}, {'n': 810, 'm': 810, 's': 'bilayer'}, {'n': 810, 'm': 810, 's': 'cylinders'}, {'n': 891, 'm': 891, 's': 'bilayer'}, {'n': 891, 'm': 891, 's': 'cylinders'}, {'n': 972, 'm': 972, 's': 'bilayer'}, {'n': 972, 'm': 972, 's': 'cylinders'}, {'n': 1053, 'm': 1053, 's': 'bilayer'}, {'n': 1053, 'm': 1053, 's': 'cylinders'}, {'n': 1134, 'm': 1134, 's': 'bilayer'}, {'n': 1134, 'm': 1134, 's': 'cylinders'}, {'n': 1215, 'm': 1215, 's': 'bilayer'}, {'n': 1215, 'm': 1215, 's': 'cylinders'}, {'n': 1296, 'm': 1296, 's': 'bilayer'}, {'n': 1296, 'm': 1296, 's': 'cylinders'}, {'n': 1377, 'm': 1377, 's': 'bilayer'}, {'n': 1377, 'm': 1377, 's': 'cylinders'}, {'n': 1458, 'm': 1458, 's': 'bilayer'}, {'n': 1458, 'm': 1458, 's': 'cylinders'}, {'n': 1539, 'm': 1539, 's': 'bilayer'}, {'n': 1539, 'm': 1539, 's': 'cylinders'}, {'n': 1620, 'm': 1620, 's': 'bilayer'}, {'n': 1620, 'm': 1620, 's': 'cylinders'}, {'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 405, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 405, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'bilayer'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8676848752d7b81fa6db67'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-50-56-222897/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-50-56-222897/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.819837', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f95a3257d270025bd0c614e'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-25-16-02-35-682237/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-25-16-02-35-682237/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.529462', 'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB on 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f8673158752d7b81fa6a964'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-15-857135/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-36-15-857135/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.949348', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f867458fd2a730dccbb400b'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-35-421040/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-35-421040/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:57.906330', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-08-932157/2020-10-13-23-31-57-903948-n-243-m-243-s-cylinders-substratepassivation', 'uuid': '53fe41c3-e92e-4752-9edd-756175877118', 'name': '2020-10-13-23-31-57-903948-n-243-m-243-s-cylinders-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-03-41-08-932157/2020-10-13-23-31-57-903948-n-243-m-243-s-cylinders-substratepassivation', 'uuid': '53fe41c3-e92e-4752-9edd-756175877118', 'name': '2020-10-13-23-31-57-903948-n-243-m-243-s-cylinders-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.187598', 'expiration_date': '2022-10-13 23:31:15.187598', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f867458fd2a730dccbb4009'}
WARNING:root:Failed reading edr for {'_id': ObjectId('5f8692fffd2a730dccbbbf88'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-52-18-373474/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-52-18-373474/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.291287', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f867a850bda12f287bb3da9'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-07-55-041308/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-07-55-041308/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.035070', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f867bd2fd2a730dccbb7218'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-13-07-785424/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-04-13-07-785424/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.119601', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f868d360bda12f287bb93c8'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-27-23-401884/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-27-23-401884/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.163404', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f86a34efd2a730dccbbdafd'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-25-418263/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-25-418263/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.736016', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-14-838046/2020-10-13-23-31-58-733049-n-1701-m-1701-s-cylinders-substratepassivation', 'uuid': 'd9ea787f-3f82-412e-b32d-ca5ad9dc5c47', 'name': '2020-10-13-23-31-58-733049-n-1701-m-1701-s-cylinders-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-07-05-14-838046/2020-10-13-23-31-58-733049-n-1701-m-1701-s-cylinders-substratepassivation', 'uuid': 'd9ea787f-3f82-412e-b32d-ca5ad9dc5c47', 'name': '2020-10-13-23-31-58-733049-n-1701-m-1701-s-cylinders-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.226133', 'expiration_date': '2022-10-13 23:31:15.226133', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f86a34efd2a730dccbbdafb'}
WARNING:root:Failed reading edr for {'_id': ObjectId('5f86d4d8beec446e55bbb803'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-10-36-48-928177/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-10-36-48-928177/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.785597', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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WARNING:root:Failed reading edr for {'_id': ObjectId('5f868d17beec446e55bb6130'), 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-30-43-388342/default.mp4', 'original_file_name': 'default.mp4', 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-30-43-388342/default.mp4', 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation', 'datetime': '2020-10-13 23:31:58.378932', 'step': 'SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad', 'source_project_id': '2020-09-27-au-111-fcc-substrate-creation', 'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad', 'metadata_fp_source_key': 'metadata->system->substrate', 'metadata_fw_dest_key': 'metadata->system->substrate', 'metadata_fw_source_key': 'metadata->system->substrate', 'description': 'CTAB 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{'n': 1701, 'm': 1701, 's': 'bilayer'}, {'n': 1701, 'm': 1701, 's': 'cylinders'}, {'n': 1782, 'm': 1782, 's': 'bilayer'}, {'n': 1782, 'm': 1782, 's': 'cylinders'}, {'n': 1863, 'm': 1863, 's': 'bilayer'}, {'n': 1863, 'm': 1863, 's': 'cylinders'}, {'n': 1944, 'm': 1944, 's': 'bilayer'}, {'n': 1944, 'm': 1944, 's': 'cylinders'}], 'system': {'counterion': {'name': 'BR', 'resname': 'BR', 'nmolecules': 1296, 'reference_atom': {'name': 'BR'}}, 'surfactant': {'name': 'CTAB', 'resname': 'CTAB', 'nmolecules': 1296, 'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]}, 'head_atom': {'name': 'N1', 'index': 17}, 'tail_atom': {'name': 'C1', 'index': 1}, 'aggregates': {'shape': 'bilayer'}, 'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001], 'radius': 11.460510481649582, 'radius_connector_atom': 6.934818490775374}, 'head_group': {'diameter': 4.525691990874208}}, 'substrate': {'element': 'Au', 'lattice_constant': 4.075, 'approximate_measures': [200.0, 200.0, 200.0], 'lmp': {'type': 11}, 'measures': [198.82074920012752, 199.633414036829, 197.62699714360895], 'name': 'AUM', 'resname': 'AUM', 'reference_atom': {'name': 'AU'}, 'length': 198.82074920012752, 'width': 199.633414036829, 'height': 197.62699714360895, 'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]], 'natoms': 463680}, 'solvent': {'name': 'H2O', 'resname': 'SOL', 'reference_atom': {'name': 'OW'}, 'height': 180.0}, 'box': {'length': 198.82074920012752, 'width': 199.633414036829, 'height': 377.62699714360895}}, 'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'}, 'element_to_pdb_atom_name_mapping': {'Au': 'AU'}, 'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}}, 'packing': {'surfactant_substrate': {'tolerance': 1.5, 'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617], [100.226, 100.354, 126.03802096329918]], 'lower_constraint_plane': 105.37984599543711, 'upper_constraint_plane': 122.27517496786207}, {'bounding_box': [[-98.572, -99.281, 126.03802096329918], [100.226, 100.354, 150.45904192659833]], 'lower_constraint_plane': 129.80086695873626, 'upper_constraint_plane': 146.69619593116124}]}}}, 'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS', 'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}, 'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-29-44-333521/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}, 'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-20-16-29-44-333521/2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation', 'uuid': '5bf4a245-17cc-4ecd-9257-47b13007e67c', 'name': '2020-10-13-23-31-58-442585-n-1296-m-1296-s-bilayer-substratepassivation'}}}, 'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation', 'creation_date': '2020-10-13 23:31:15.214088', 'expiration_date': '2022-10-13 23:31:15.214088', 'type': 'mp4_file'}, 'compressed': True, 'gfs_id': '5f8f1416dd26cd5935f45ebc'}

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-66-44729cd44db4> in <module>
     39 print('')
     40 
---> 41 res_mi_df = pd.concat(res_mi_list)
     42 res_df = res_mi_df.reset_index()

/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
    269     ValueError: Indexes have overlapping values: ['a']
    270     """
--> 271     op = _Concatenator(
    272         objs,
    273         axis=axis,

/usr/local/lib/python3.8/dist-packages/pandas/core/reshape/concat.py in __init__(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)
    327 
    328         if len(objs) == 0:
--> 329             raise ValueError("No objects to concatenate")
    330 
    331         if keys is None:

ValueError: No objects to concatenate

res_mi_df

y_quantities = [
    'Potential',
    'Pressure',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

positions = [
    (0,0),
    (0,1),
    (1,0),
    (2,0),
    (2,1),
]
fig, ax = plt.subplots(3,2,figsize=(10,12))
for key, grp in res_df.groupby(parameter_keys[0]):
    for y_quantity, position in zip(y_quantities, positions):
        grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        
fig.tight_layout()

Visualize trajectory¶

query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsEnergyMinimizationAfterSolvation'},
    'metadata.type': 'mp4_file',
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

44

# check

aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'nmolecules': '$metadata.system.surfactant.nmolecules'
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

# for i, c in enumerate(cursor): 
#    content, metadata = fp.get_file_by_id(c["latest"])
#    nmolecules = int(c["_id"]["nmolecules"])
    

res = [ {**c['_id'], **c} for c in cursor]
columns = ['nmolecules', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

parameter_keys

['nmolecules', 'shape']

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        obj_dict.update({c["_id"][parameter_keys[0]]: Video.from_file(tmp.name)})
    print('.',end='')

............................................

c

{'_id': {'nmolecules': 81, 'shape': 'bilayer'},
 'degeneracy': 1,
 'latest': '5f8676eafd2a730dccbb56ff'}

for key, obj in obj_dict.items():
    print(key)
    display(obj)

NVT equilibration analysis¶

Overview on objects in step¶

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'}
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

631

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Global observables¶

query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)

30

parameter_dict = {
    'nmolecules': 'metadata.system.surfactant.nmolecules',
    'shape': 'metadata.system.surfactant.aggregates.shape'
}

parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res_list = []

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [ *[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()

..............................

res_df.columns

Index(['nmolecules', 'shape', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')

res_df_mi

#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        
fig.tight_layout()

<ipython-input-117-bb605528b000>:24: UserWarning: Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations
  fig.tight_layout()

Visualize trajectory¶

query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNVTEquilibration'},
    'metadata.type': 'mp4_file',
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

30

#parameter_dict = {'nmolecules': 'metadata.system.surfactant.nmolecules'}
#parameter_dict = {'shape': 'metadata.system.surfactant.aggregates.shape'}
parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')

..............................

for key, obj in obj_dict.items():
    print(key)
    display(obj)

('cylinders', 1053)

('cylinders', 324)

('cylinders', 162)

('cylinders', 405)

('cylinders', 243)

('cylinders', 567)

('cylinders', 648)

('cylinders', 486)

('cylinders', 81)

('cylinders', 729)

NPT equilibration analysis¶

Overview on objects in step¶

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration:push_filepad'}
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

567

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Global observables¶

query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)

27

metadata = fp.filepad.find_one(query)

metadata

{'_id': ObjectId('5f8687378752d7b81fa747ec'),
 'identifier': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-57-308899/default.edr',
 'original_file_name': 'default.edr',
 'original_file_path': '/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-57-308899/default.edr',
 'metadata': {'project': '2020-10-13-ctab-on-au-111-substrate-passivation',
  'datetime': '2020-10-13 23:31:58.151029',
  'step': 'SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad',
  'source_project_id': '2020-09-27-au-111-fcc-substrate-creation',
  'source_step': 'FCCSubstrateCreationChainWorkflowGenerator:LAMMPSEquilibrationNPTWorkflowGenerator:push_filepad',
  'metadata_fp_source_key': 'metadata->system->substrate',
  'metadata_fw_dest_key': 'metadata->system->substrate',
  'metadata_fw_source_key': 'metadata->system->substrate',
  'description': 'CTAB on Au(111) substrate passivation',
  'owners': [{'name': 'Johannes Laurin Hörmann',
    'email': 'johannes.hoermann@imtek.uni-freiburg.de',
    'username': 'fr_jh1130',
    'orcid': '0000-0001-5867-695X'}],
  'machine': 'juwels',
  'mode': 'production',
  'parameter_label_key_dict': {'n': 'system->surfactant->nmolecules',
   'm': 'system->counterion->nmolecules',
   's': 'system->surfactant->aggregates->shape'},
  'parameter_values': [{'n': 81, 'm': 81, 's': 'bilayer'},
   {'n': 81, 'm': 81, 's': 'cylinders'},
   {'n': 162, 'm': 162, 's': 'bilayer'},
   {'n': 162, 'm': 162, 's': 'cylinders'},
   {'n': 243, 'm': 243, 's': 'bilayer'},
   {'n': 243, 'm': 243, 's': 'cylinders'},
   {'n': 324, 'm': 324, 's': 'bilayer'},
   {'n': 324, 'm': 324, 's': 'cylinders'},
   {'n': 405, 'm': 405, 's': 'bilayer'},
   {'n': 405, 'm': 405, 's': 'cylinders'},
   {'n': 486, 'm': 486, 's': 'bilayer'},
   {'n': 486, 'm': 486, 's': 'cylinders'},
   {'n': 567, 'm': 567, 's': 'bilayer'},
   {'n': 567, 'm': 567, 's': 'cylinders'},
   {'n': 648, 'm': 648, 's': 'bilayer'},
   {'n': 648, 'm': 648, 's': 'cylinders'},
   {'n': 729, 'm': 729, 's': 'bilayer'},
   {'n': 729, 'm': 729, 's': 'cylinders'},
   {'n': 810, 'm': 810, 's': 'bilayer'},
   {'n': 810, 'm': 810, 's': 'cylinders'},
   {'n': 891, 'm': 891, 's': 'bilayer'},
   {'n': 891, 'm': 891, 's': 'cylinders'},
   {'n': 972, 'm': 972, 's': 'bilayer'},
   {'n': 972, 'm': 972, 's': 'cylinders'},
   {'n': 1053, 'm': 1053, 's': 'bilayer'},
   {'n': 1053, 'm': 1053, 's': 'cylinders'},
   {'n': 1134, 'm': 1134, 's': 'bilayer'},
   {'n': 1134, 'm': 1134, 's': 'cylinders'},
   {'n': 1215, 'm': 1215, 's': 'bilayer'},
   {'n': 1215, 'm': 1215, 's': 'cylinders'},
   {'n': 1296, 'm': 1296, 's': 'bilayer'},
   {'n': 1296, 'm': 1296, 's': 'cylinders'},
   {'n': 1377, 'm': 1377, 's': 'bilayer'},
   {'n': 1377, 'm': 1377, 's': 'cylinders'},
   {'n': 1458, 'm': 1458, 's': 'bilayer'},
   {'n': 1458, 'm': 1458, 's': 'cylinders'},
   {'n': 1539, 'm': 1539, 's': 'bilayer'},
   {'n': 1539, 'm': 1539, 's': 'cylinders'},
   {'n': 1620, 'm': 1620, 's': 'bilayer'},
   {'n': 1620, 'm': 1620, 's': 'cylinders'},
   {'n': 1701, 'm': 1701, 's': 'bilayer'},
   {'n': 1701, 'm': 1701, 's': 'cylinders'},
   {'n': 1782, 'm': 1782, 's': 'bilayer'},
   {'n': 1782, 'm': 1782, 's': 'cylinders'},
   {'n': 1863, 'm': 1863, 's': 'bilayer'},
   {'n': 1863, 'm': 1863, 's': 'cylinders'},
   {'n': 1944, 'm': 1944, 's': 'bilayer'},
   {'n': 1944, 'm': 1944, 's': 'cylinders'}],
  'system': {'counterion': {'name': 'BR',
    'resname': 'BR',
    'nmolecules': 729,
    'reference_atom': {'name': 'BR'}},
   'surfactant': {'name': 'CTAB',
    'resname': 'CTAB',
    'nmolecules': 729,
    'connector_atom': {'index': 15, 'position': [-5.899, -0.206, -0.002]},
    'head_atom': {'name': 'N1', 'index': 17},
    'tail_atom': {'name': 'C1', 'index': 1},
    'aggregates': {'shape': 'bilayer'},
    'bounding_sphere': {'center': [1.0285000000000029, 0.1125, 0.001],
     'radius': 11.460510481649582,
     'radius_connector_atom': 6.934818490775374},
    'head_group': {'diameter': 4.525691990874208}},
   'substrate': {'element': 'Au',
    'lattice_constant': 4.075,
    'approximate_measures': [200.0, 200.0, 200.0],
    'lmp': {'type': 11},
    'measures': [198.82074920012752, 199.633414036829, 197.62699714360895],
    'name': 'AUM',
    'resname': 'AUM',
    'reference_atom': {'name': 'AU'},
    'length': 198.82074920012752,
    'width': 199.633414036829,
    'height': 197.62699714360895,
    'bounding_box': [[-98.572, -99.281, -97.52], [100.226, 100.354, 100.117]],
    'natoms': 463680},
   'solvent': {'name': 'H2O',
    'resname': 'SOL',
    'reference_atom': {'name': 'OW'},
    'height': 180.0},
   'box': {'length': 198.82074920012752,
    'width': 199.633414036829,
    'height': 377.62699714360895}},
  'step_specific': {'conversion': {'lmp_type_to_element_mapping': {'11': 'Au'},
    'element_to_pdb_atom_name_mapping': {'Au': 'AU'},
    'element_to_pdb_residue_name_mapping': {'Au': 'AUM'}},
   'packing': {'surfactant_substrate': {'tolerance': 1.5,
     'constraints': {'layers': [{'bounding_box': [[-98.572, -99.281, 101.617],
         [100.226, 100.354, 126.03802096329918]],
        'lower_constraint_plane': 105.37984599543711,
        'upper_constraint_plane': 122.27517496786207},
       {'bounding_box': [[-98.572, -99.281, 126.03802096329918],
         [100.226, 100.354, 150.45904192659833]],
        'lower_constraint_plane': 129.80086695873626,
        'upper_constraint_plane': 146.69619593116124}]}}},
   'dtool_push': {'dtool_target': '/p/project/chfr13/hoermann4/dtool/DATASETS',
    'remote_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/project/chfr13/hoermann4/dtool/DATASETS/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'},
    'local_proto_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-49-886038/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'},
    'local_frozen_dataset': {'uri': 'file://juwels01.ib.juwels.fzj.de/p/scratch/chfr13/hoermann/fireworks/launchpad/launcher_2020-10-14-05-05-49-886038/2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation',
     'uuid': '45ff7396-71ce-4b63-b90b-93e395d2bde6',
     'name': '2020-10-13-23-31-58-148727-n-729-m-729-s-bilayer-substratepassivation'}}},
  'project_id': '2020-10-13-ctab-on-au-111-substrate-passivation',
  'creation_date': '2020-10-13 23:31:15.200230',
  'expiration_date': '2022-10-13 23:31:15.200230',
  'type': 'energy_file'},
 'compressed': True,
 'gfs_id': '5f8687378752d7b81fa747ea'}

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

[ c for c in cursor]

[{'_id': {'shape': 'bilayer', 'nmolecules': 972},
  'degeneracy': 1,
  'latest': '5f86967ffd2a730dccbbc7b8'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 567},
  'degeneracy': 1,
  'latest': '5f8692fb6b7f8f8ab3bbe5b5'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 243},
  'degeneracy': 1,
  'latest': '5f868b04beec446e55bb4f8c'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 1053},
  'degeneracy': 1,
  'latest': '5f86ac660bda12f287bbe0af'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 729},
  'degeneracy': 1,
  'latest': '5f86a860beec446e55bbae82'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 486},
  'degeneracy': 1,
  'latest': '5f86930cfd2a730dccbbbf8e'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 243},
  'degeneracy': 1,
  'latest': '5f868c31beec446e55bb57dc'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 324},
  'degeneracy': 1,
  'latest': '5f868b2f0bda12f287bb715d'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 162},
  'degeneracy': 1,
  'latest': '5f868c0afd2a730dccbb8c45'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 81},
  'degeneracy': 1,
  'latest': '5f868e628752d7b81fa771b2'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 810},
  'degeneracy': 1,
  'latest': '5f86a9bc0bda12f287bbd884'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 405},
  'degeneracy': 1,
  'latest': '5f8689366b7f8f8ab3bbda9a'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1296},
  'degeneracy': 1,
  'latest': '5f95a3e74e2af1e9d00ff6ea'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 972},
  'degeneracy': 1,
  'latest': '5f86d4fe8752d7b81fa78c57'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 162},
  'degeneracy': 1,
  'latest': '5f868cdbfd2a730dccbb946c'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 81},
  'degeneracy': 1,
  'latest': '5f868d1abeec446e55bb6136'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 648},
  'degeneracy': 1,
  'latest': '5f8688566b7f8f8ab3bbd204'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1053},
  'degeneracy': 1,
  'latest': '5f95a6654e2af1e9d00fff1e'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 891},
  'degeneracy': 1,
  'latest': '5f869ae58752d7b81fa7831f'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 810},
  'degeneracy': 1,
  'latest': '5f8687d38752d7b81fa75013'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 648},
  'degeneracy': 1,
  'latest': '5f86935c6b7f8f8ab3bbee25'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 567},
  'degeneracy': 1,
  'latest': '5f8687d26b7f8f8ab3bbc9df'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 324},
  'degeneracy': 1,
  'latest': '5f8689358752d7b81fa76087'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 729},
  'degeneracy': 1,
  'latest': '5f8687378752d7b81fa747ea'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 486},
  'degeneracy': 1,
  'latest': '5f8688578752d7b81fa7583f'},
 {'_id': {'shape': 'cylinders', 'nmolecules': 405},
  'degeneracy': 1,
  'latest': '5f8688db0bda12f287bb68ea'},
 {'_id': {'shape': 'bilayer', 'nmolecules': 1944},
  'degeneracy': 1,
  'latest': '5f95951c7d270025bd0bc7ff'}]

res_list = []

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [*[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()

...........................

res_df.columns

Index(['shape', 'nmolecules', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Box-X',
       'Box-Y', 'Box-Z', 'Volume', 'Density', 'pV', 'Enthalpy', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')

res_df_mi

#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Volume',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        # grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        grp.plot('Time',y_quantity,ax=ax[position],legend=False,title=y_quantity)
        
fig.tight_layout()

Visualize trajectory¶

query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsNPTEquilibration'},
    'metadata.type': 'mp4_file',
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

27

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        # obj_list.append(Video(filename=tmp.name)) 
        # obj_list.append(tmp.name)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')

...........................

for key, obj in obj_dict.items():
    print(key)
    display(obj)

('cylinders', 972)

('cylinders', 648)

('cylinders', 324)

('cylinders', 405)

('cylinders', 567)

('cylinders', 243)

('cylinders', 1053)

('cylinders', 729)

('cylinders', 486)

('cylinders', 162)

Pre-evaluated RDF¶

Overview¶

query = { 
    "metadata.project": project_id,
    "metadata.type": {'$regex': '.*rdf$'},
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)

243

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Substrate - surfactant head RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)

27

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    # res_list.append(data)
    print('.',end='')
print('')

...........................

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Substrate - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)

27

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}


aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

...........................

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
    
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsNPTEquilibration"},
}

fp.filepad.count_documents(query)

27

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}

aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

...........................

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['nmolecules']):
for pos, (nmolecules, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(nmolecules)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Relaxation analysis¶

Overview on objects in step¶

# queries to the data base are simple dictionaries
query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'}
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

383

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
                'name': '$metadata.name',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'name', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Global observables¶

query = { 
    "metadata.project": project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'},
    "metadata.type":    'energy_file',
}
fp.filepad.count_documents(query)

74

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res_list = []

cursor = fp.filepad.aggregate(aggregation_pipeline)

for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    with tempfile.NamedTemporaryFile(suffix='.edr') as tmp:
        tmp.write(content)
        res_df = panedr.edr_to_df(tmp.name)
        
        mi = pd.MultiIndex.from_product(
            [*[[v] for v in c["_id"].values()],res_df.index],
            names=[*c["_id"].keys(),'step'])
        res_mi_df = res_df.set_index(mi)
        res_list.append(res_mi_df)
    print('.',end='')
print('')
res_df_mi = pd.concat(res_list)
res_df = res_df_mi.reset_index()

........................

res_df.columns

Index(['shape', 'nmolecules', 'step', 'Time', 'Bond', 'U-B', 'Proper Dih.',
       'LJ-14', 'Coulomb-14', 'LJ (SR)', 'Coulomb (SR)', 'Coul. recip.',
       'Position Rest.', 'Potential', 'Kinetic En.', 'Total Energy',
       'Conserved En.', 'Temperature', 'Pressure', 'Constr. rmsd', 'Box-X',
       'Box-Y', 'Box-Z', 'Volume', 'Density', 'pV', 'Enthalpy', 'Vir-XX',
       'Vir-XY', 'Vir-XZ', 'Vir-YX', 'Vir-YY', 'Vir-YZ', 'Vir-ZX', 'Vir-ZY',
       'Vir-ZZ', 'Pres-XX', 'Pres-XY', 'Pres-XZ', 'Pres-YX', 'Pres-YY',
       'Pres-YZ', 'Pres-ZX', 'Pres-ZY', 'Pres-ZZ', '#Surf*SurfTen',
       'Coul-SR:Surfactant-Surfactant', 'LJ-SR:Surfactant-Surfactant',
       'Coul-14:Surfactant-Surfactant', 'LJ-14:Surfactant-Surfactant',
       'Coul-SR:Surfactant-Substrate', 'LJ-SR:Surfactant-Substrate',
       'Coul-14:Surfactant-Substrate', 'LJ-14:Surfactant-Substrate',
       'Coul-SR:Surfactant-Ion', 'LJ-SR:Surfactant-Ion',
       'Coul-14:Surfactant-Ion', 'LJ-14:Surfactant-Ion',
       'Coul-SR:Surfactant-rest', 'LJ-SR:Surfactant-rest',
       'Coul-14:Surfactant-rest', 'LJ-14:Surfactant-rest',
       'Coul-SR:Substrate-Substrate', 'LJ-SR:Substrate-Substrate',
       'Coul-14:Substrate-Substrate', 'LJ-14:Substrate-Substrate',
       'Coul-SR:Substrate-Ion', 'LJ-SR:Substrate-Ion', 'Coul-14:Substrate-Ion',
       'LJ-14:Substrate-Ion', 'Coul-SR:Substrate-rest', 'LJ-SR:Substrate-rest',
       'Coul-14:Substrate-rest', 'LJ-14:Substrate-rest', 'Coul-SR:Ion-Ion',
       'LJ-SR:Ion-Ion', 'Coul-14:Ion-Ion', 'LJ-14:Ion-Ion', 'Coul-SR:Ion-rest',
       'LJ-SR:Ion-rest', 'Coul-14:Ion-rest', 'LJ-14:Ion-rest',
       'Coul-SR:rest-rest', 'LJ-SR:rest-rest', 'Coul-14:rest-rest',
       'LJ-14:rest-rest', 'T-non-Substrate', 'T-Substrate',
       'Lamb-non-Substrate', 'Lamb-Substrate'],
      dtype='object')

res_df_mi

#n = len(res_df['nmolecules'].unique())
y_quantities = [
    'Temperature',
    'Pressure',
    'Volume',
    'Potential',
    'Bond',
    'Coulomb (SR)',
    'Coul. recip.',
    ]

n = len(y_quantities)
cols = 2
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for key, grp in res_df.groupby(parameter_keys):
    for y_quantity, position in zip(y_quantities, positions):
        # grp.plot('Time',y_quantity,ax=ax[position],label=key,title=y_quantity)
        grp.plot('Time', y_quantity, ax=ax[position], legend=False, title=y_quantity)
        
fig.tight_layout()

Visualize trajectory¶

query = {
    'metadata.project': project_id,
    'metadata.step': {'$regex': 'GromacsRelaxation'},
    'metadata.type': 'mp4_file',
}

# use underlying MongoDB functionality to check total number of documents matching query
fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

aggregation_pipeline = [
    {
        "$match": query
    },
    {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    },
    { 
        "$group": { 
            "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
            "degeneracy": {"$sum": 1}, # number matching data sets
            "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
        }
    },
    {
        "$sort": { 
            "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
        }
    },
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

obj_dict = {}
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    # print(metadata['metadata'])
    with tempfile.NamedTemporaryFile(suffix='.mp4',delete=False) as tmp:
        tmp.write(content)
        # obj_list.append(Video(filename=tmp.name)) 
        # obj_list.append(tmp.name)
        key = tuple(c["_id"].values())
        obj_dict.update({key: Video.from_file(tmp.name)})
    print('.',end='')

........

for key, obj in obj_dict.items():
    print(key)
    display(obj)

('cylinders', 648)

('cylinders', 486)

('cylinders', 567)

('cylinders', 243)

('bilayer', 567)

('bilayer', 324)

('bilayer', 648)

('bilayer', 729)

Pre-evaluated RDF¶

Overview¶

query = { 
    "metadata.project": project_id,
    "metadata.type": {'$regex': '.*rdf$'},
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

72

# check files degenerate by 'metadata.type' ad 'metadata.name'
aggregation_pipeline = [
    {
        "$match": query
    },
    {  # group by unique project id
        "$group": { 
            "_id": { 
                'type': '$metadata.type',
            },
            "object_count": {"$sum": 1}, # count matching data sets
            "earliest":  {'$min': '$metadata.datetime' },
            "latest":  {'$max': '$metadata.datetime' },
        },
    },
    {  # sort by earliest date, descending
        "$sort": { 
            "earliest": pymongo.DESCENDING,
        }
    }
]

cursor = fp.filepad.aggregate(aggregation_pipeline)

res = [ {**c['_id'], **c} for c in cursor]
columns = ['type', 'earliest', 'latest', 'object_count', '_id']
res_df = pd.DataFrame(data=res, columns=columns) # pandas Dataframe is just nice for printing in notebook
del res_df["_id"]

res_df

Substrate - surfactant head RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Substrate - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'substrate_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}


aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
    
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
second_sort_aggregation = {
    "$sort": { 
        "_id.{}".format(parameter_keys[0]): pymongo.DESCENDING,
    }
}

aggregation_pipeline = [ 
    match_aggregation, sort_aggregation, group_aggregation, second_sort_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['nmolecules']):
for pos, (nmolecules, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(nmolecules)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant head - surfactant head RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_head_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Surfactant tail - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'surfactant_tail_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - surfactant head RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_surfactant_head_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - surfactant tail RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_surfactant_tail_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - substrate RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_substrate_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'],data['rdf'][0], label='First frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][len(data)//2],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'],data['rdf'][-1],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'],data['rdf'][-1],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

Counterion - counterion RDF¶

query = { 
    "metadata.project": project_id,
    "metadata.type": 'counterion_counterion_rdf',
    "metadata.step": {'$regex': "GromacsRelaxation"},
}

fp.filepad.count_documents(query)

8

parameter_dict = {
    'shape': 'metadata.system.surfactant.aggregates.shape',
    'nmolecules': 'metadata.system.surfactant.nmolecules'
}
parameter_keys = list(parameter_dict.keys())

res_dict = {}
failed_list = []

match_aggregation = {
        "$match": query
    }
sort_aggregation = {
        "$sort": { 
            "metadata.datetime": pymongo.DESCENDING,
        }
    }
group_aggregation = { 
    "$group": { 
        "_id": { field: '${}'.format(key) for field, key in parameter_dict.items() },
        "degeneracy": {"$sum": 1}, # number matching data sets
        "latest":     {"$first": "$gfs_id"} # unique gridfs id of file
    }
}
aggregation_pipeline = [ match_aggregation, sort_aggregation, group_aggregation ]
cursor = fp.filepad.aggregate(aggregation_pipeline)

# res_list = []
for i, c in enumerate(cursor): 
    content, metadata = fp.get_file_by_id(c["latest"])
    parameter_values = tuple(c["_id"][parameter_key] for parameter_key in parameter_keys)
    data_str = io.StringIO(content.decode())
    data = np.loadtxt(data_str, comments='#')
    d = data[0] # distance bins
    rdf = data[1:]
    res_dict[parameter_values] = {'dist': d, 'rdf': rdf}
    print('.',end='')
print('')

........

n = len(res_dict)
cols = 2 if n > 1 else 1
rows = round(n/cols)
if rows > 1:
    positions = [(i,j) for i in range(rows) for j in range(cols)][:n]
else:
    positions = [i for i in range(cols)][:n]
    
fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
if not isinstance(ax, Iterable):
    ax = [ax]
# for key, grp in res_df.groupby(['parameter_key']):
for pos, (parameter_key, data) in zip(positions, res_dict.items()):
    ax[pos].plot(data['dist'][1:],data['rdf'][0][1:], label='First frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][len(data)//2][1:],label='Intermediate frame RDF')
    ax[pos].plot(data['dist'][1:],data['rdf'][-1][1:],label='Last frame RDF')
    ax[pos].set_title(parameter_key)
    ax[pos].legend()

fig.tight_layout()
# fig.legend()
fig.show()

n = 1
cols = 2 if n > 1 else 1
rows = round(n/cols)

fig, ax = plt.subplots(rows,cols,figsize=(5*cols,4*rows))
for (parameter_key, data) in res_dict.items():
    ax.plot(data['dist'][1:],data['rdf'][-1][1:],label=parameter_key)
    ax.legend()

fig.tight_layout()
# fig.legend()
fig.show()

	object_count	earliest	latest	project
0	72	2020-10-25 01:48:28.113800	2020-10-25 01:48:28.245721	2020-10-25-sds-on-au-111-substrate-passivation-trial
1	97	2020-10-24 19:55:53.929728	2020-10-25 00:55:09.723289	2020-10-24-sds-on-au-111-substrate-passivation-trial
2	53	2020-10-24 19:50:57.364604	2020-10-24 19:50:57.367249	2020-10-24-au-111-150x150x150-fcc-substrate-creation
3	53	2020-10-20 00:36:42.139788	2020-10-20 00:36:42.145747	2020-10-19-au-111-150x150x150-fcc-substrate-creation
4	2815	2020-10-13 23:31:57.716886	2020-10-13 23:31:58.871696	2020-10-13-ctab-on-au-111-substrate-passivation
5	167	2020-10-11 00:52:32.501863	2020-10-11 21:47:34.277020	2020-10-11-ctab-on-au-111-substrate-passivation-trial
6	9	2020-10-10 19:02:26.582714	2020-10-10 19:02:26.667597	2020-10-10-ctab-on-au-111-substrate-passivation-trial
7	68	2020-10-05 23:58:54.069384	2020-10-05 23:58:54.150170	2020-10-05-ctab-on-au-111-substrate-passivation-trial
8	68	2020-10-03 13:58:43.057925	2020-10-03 13:58:43.176783	2020-10-03-ctab-on-au-111-substrate-passivation-trial
9	3	2020-10-02 20:17:13.935637	2020-10-02 20:17:14.015525	2020-10-02-ctab-on-au-111-substrate-passivation-trial
10	6	2020-10-01 16:38:35.447564	2020-10-01 21:49:44.957275	2020-10-01-ctab-on-au-111-substrate-passivation-trial
11	3	2020-09-30 00:59:24.296631	2020-09-30 00:59:24.381181	2020-09-30-ctab-on-au-111-substrate-passivation-trial
12	2703	2020-09-28 02:11:38.861517	2020-09-28 02:11:42.558642	2020-09-28-ctab-on-au-111-substrate-passivation
13	53	2020-09-27 18:58:47.134481	2020-09-27 18:58:47.137826	2020-09-27-au-111-fcc-substrate-creation
14	132	2020-09-27 18:39:55.970548	2020-09-27 18:39:56.179259	2020-09-27-ctab-on-au-111-substrate-passivation-trial
15	53	2020-09-26 14:45:31.896748	2020-09-26 14:45:31.898524	2020-09-26-au-111-fcc-substrate-creation-trial
16	92	2020-09-26 00:31:02.102804	2020-09-26 00:31:02.270975	2020-09-25-ctab-on-au-111-substrate-passivation
17	80	2020-09-25 19:25:17.206266	2020-09-25 23:20:46.761970	2020-09-25-au-111-fcc-substrate-creation-trial
18	56	2020-09-25 19:07:28.245703	2020-09-26 00:33:42.499737	2020-09-25-au-111-fcc-substrate-creation
19	2844	2020-09-14 19:40:24.649384	2020-09-14 19:40:26.998397	2020-09-14-sds-on-au-111-substrate-passivation
20	421	2020-09-09 23:24:22.512782	2020-09-09 23:24:23.635704	2020-09-10-sds-on-au-111-substrate-passivation-trial
21	210	2020-09-08 23:15:38.029121	2020-09-09 17:35:18.670720	2020-09-09-sds-on-au-111-substrate-passivation-trial
22	252	2020-09-08 18:12:59.181303	2020-09-08 18:12:59.406524	2020-09-08-sds-on-au-111-substrate-passivation-trial
23	343	2020-09-03 15:46:52.139300	2020-09-03 23:22:15.222281	2020-09-03-sds-on-au-111-substrate-passivation-trial
24	245	2020-09-01 16:07:48.182428	2020-09-02 15:39:12.955771	2020-09-01-sds-on-au-111-substrate-passivation-trial
25	52	2020-08-31 02:32:35.171803	2020-09-01 00:35:40.345368	2020-08-31-sds-on-au-111-substrate-passivation-trial
26	3	2020-08-31 01:32:13.820858	2020-08-31 01:32:13.902597	2020-08-30-sds-on-au-111-substrate-passivation-trial
27	6	2020-08-28 00:14:08.820442	2020-08-28 00:35:31.724026	2020-08-27-sds-on-au-111-substrate-passivation-trial
28	80	2020-08-24 17:48:58.997210	2020-08-24 20:24:33.489028	2020-08-24-au-111-fcc-substrate-creation-trial
29	537	2020-07-29 03:50:20.375090	2020-07-29 03:50:22.884335	2020-07-29-ctab-on-au-111-indenter-passivation
30	399	2020-07-29 03:47:40.301419	2020-07-29 03:47:42.358240	2020-07-29-sds-on-au-111-indenter-passivation

	type	step	name	earliest	latest	object_count
0	mp4_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943535	2020-10-13 23:31:58.157138	4
1	surfactant_tail_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943533	2020-10-13 23:31:58.157136	4
2	surfactant_head_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943531	2020-10-13 23:31:58.157133	4
3	substrate_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943528	2020-10-13 23:31:58.157131	4
4	counterion_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943526	2020-10-13 23:31:58.157128	4
5	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943524	2020-10-13 23:31:58.157126	4
6	surfactant_head_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943522	2020-10-13 23:31:58.157124	4
7	surfactant_head_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943520	2020-10-13 23:31:58.157122	4
8	substrate_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943517	2020-10-13 23:31:58.157120	4
9	substrate_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943515	2020-10-13 23:31:58.157117	4
10	counterion_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943513	2020-10-13 23:31:58.157115	4
11	counterion_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943511	2020-10-13 23:31:58.157113	4
12	counterion_substrate_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943508	2020-10-13 23:31:58.157111	4
13	counterion_counterion_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943506	2020-10-13 23:31:58.157108	4
14	index_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943504	2020-10-13 23:31:58.157106	4
15	run_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943502	2020-10-13 23:31:58.157104	4
16	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943499	2020-10-13 23:31:58.157102	4
17	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943497	2020-10-13 23:31:58.157099	4
18	trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943495	2020-10-13 23:31:58.157097	4
19	uncompressed_trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.943492	2020-10-13 23:31:58.157095	4
20	mp4_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921402	2020-10-13 23:31:58.135382	4
21	surfactant_tail_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921399	2020-10-13 23:31:58.135380	4
22	surfactant_head_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921397	2020-10-13 23:31:58.135377	4
23	substrate_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921395	2020-10-13 23:31:58.135375	4
24	counterion_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921392	2020-10-13 23:31:58.135373	4
25	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921390	2020-10-13 23:31:58.135371	4
26	surfactant_head_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921388	2020-10-13 23:31:58.135368	4
27	surfactant_head_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921386	2020-10-13 23:31:58.135366	4
28	substrate_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921383	2020-10-13 23:31:58.135364	4
29	substrate_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921381	2020-10-13 23:31:58.135361	4
30	counterion_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921379	2020-10-13 23:31:58.135359	4
31	counterion_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921376	2020-10-13 23:31:58.135357	4
32	counterion_substrate_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921374	2020-10-13 23:31:58.135355	4
33	counterion_counterion_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921372	2020-10-13 23:31:58.135353	4
34	index_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921370	2020-10-13 23:31:58.135350	4
35	run_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921367	2020-10-13 23:31:58.135348	4
36	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921365	2020-10-13 23:31:58.135346	4
37	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921363	2020-10-13 23:31:58.135344	4
38	trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921361	2020-10-13 23:31:58.135342	4
39	uncompressed_trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.921358	2020-10-13 23:31:58.135339	4
40	energy_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.836888	2020-10-13 23:31:58.351891	42
41	log_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.836885	2020-10-13 23:31:58.351888	42
42	checkpoint_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.836878	2020-10-13 23:31:58.351883	42
43	mp4_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830754	2020-10-13 23:31:58.346478	12
44	surfactant_tail_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830752	2020-10-13 23:31:58.346476	12
45	surfactant_head_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830749	2020-10-13 23:31:58.346474	12
46	substrate_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830747	2020-10-13 23:31:58.346472	12
47	counterion_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830745	2020-10-13 23:31:58.346469	12
48	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830743	2020-10-13 23:31:58.346467	12
49	surfactant_head_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830740	2020-10-13 23:31:58.346465	12
50	surfactant_head_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830738	2020-10-13 23:31:58.346463	12
51	substrate_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830736	2020-10-13 23:31:58.346461	12
52	substrate_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830734	2020-10-13 23:31:58.346459	12
53	counterion_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830732	2020-10-13 23:31:58.346457	12
54	counterion_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830729	2020-10-13 23:31:58.346454	12
55	counterion_substrate_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830727	2020-10-13 23:31:58.346452	12
56	counterion_counterion_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830725	2020-10-13 23:31:58.346450	12
57	run_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830723	2020-10-13 23:31:58.346448	12
58	index_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830721	2020-10-13 23:31:58.346446	12
59	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830718	2020-10-13 23:31:58.346443	12
60	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830716	2020-10-13 23:31:58.346441	12
61	trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830714	2020-10-13 23:31:58.346439	12
62	energy_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830711	2020-10-13 23:31:58.346436	12
63	log_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.830704	2020-10-13 23:31:58.346430	12
64	mp4_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825856	2020-10-13 23:31:58.642317	13
65	surfactant_tail_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825854	2020-10-13 23:31:58.642311	13
66	surfactant_head_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825852	2020-10-13 23:31:58.642305	13
67	substrate_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825849	2020-10-13 23:31:58.642300	13
68	counterion_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825847	2020-10-13 23:31:58.642294	13
69	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825845	2020-10-13 23:31:58.642288	13
70	surfactant_head_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825843	2020-10-13 23:31:58.642282	13
71	surfactant_head_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825840	2020-10-13 23:31:58.642276	13
72	substrate_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825838	2020-10-13 23:31:58.642270	13
73	substrate_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825836	2020-10-13 23:31:58.642264	13
74	counterion_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825833	2020-10-13 23:31:58.642258	13
75	counterion_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825831	2020-10-13 23:31:58.642252	13
76	counterion_substrate_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825829	2020-10-13 23:31:58.642247	13
77	counterion_counterion_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825826	2020-10-13 23:31:58.642241	13
78	run_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825824	2020-10-13 23:31:58.642236	13
79	index_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825822	2020-10-13 23:31:58.642230	13
80	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825819	2020-10-13 23:31:58.642223	13
81	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825817	2020-10-13 23:31:58.642217	13
82	trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825815	2020-10-13 23:31:58.642211	13
83	energy_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825811	2020-10-13 23:31:58.642204	13
84	log_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.825805	2020-10-13 23:31:58.642192	13
85	mp4_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819837	2020-10-13 23:31:58.871696	23
86	surfactant_tail_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819835	2020-10-13 23:31:58.871693	23
87	surfactant_head_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819832	2020-10-13 23:31:58.871691	23
88	substrate_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819830	2020-10-13 23:31:58.871689	23
89	counterion_rmsd	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819828	2020-10-13 23:31:58.871687	23
90	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819826	2020-10-13 23:31:58.871685	23
91	surfactant_head_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819823	2020-10-13 23:31:58.871682	23
92	surfactant_head_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819821	2020-10-13 23:31:58.871680	23
93	substrate_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819819	2020-10-13 23:31:58.871678	23
94	substrate_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819817	2020-10-13 23:31:58.871676	23
95	counterion_surfactant_tail_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819814	2020-10-13 23:31:58.871674	23
96	counterion_surfactant_head_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819812	2020-10-13 23:31:58.871671	23
97	counterion_substrate_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819810	2020-10-13 23:31:58.871669	23
98	counterion_counterion_rdf	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819807	2020-10-13 23:31:58.871667	23
99	trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819805	2020-10-13 23:31:58.871665	23
100	run_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819803	2020-10-13 23:31:58.871663	23
101	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819801	2020-10-13 23:31:58.871660	23
102	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819798	2020-10-13 23:31:58.871658	23
103	uncompressed_trajectory_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819796	2020-10-13 23:31:58.871656	23
104	energy_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819793	2020-10-13 23:31:58.871653	23
105	log_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.819787	2020-10-13 23:31:58.871647	23
106	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad	NaN	2020-10-13 23:31:57.815068	2020-10-13 23:31:58.866987	24
107	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad	NaN	2020-10-13 23:31:57.815064	2020-10-13 23:31:58.866984	24
108	topology_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad	NaN	2020-10-13 23:31:57.814935	2020-10-13 23:31:58.866857	24
109	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad	NaN	2020-10-13 23:31:57.814932	2020-10-13 23:31:58.866854	24
110	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:PDBCleanup:push_filepad	NaN	2020-10-13 23:31:57.814621	2020-10-13 23:31:58.866480	24
111	data_file	SubstratePassivation:CylindricalPackingAndEquilibartion:CylindricalPacking:CylindricalPackingMain:push_filepad	NaN	2020-10-13 23:31:57.814415	2020-10-13 23:31:58.866236	24
112	energy_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.814034	2020-10-13 23:31:58.865832	32
113	log_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.814031	2020-10-13 23:31:58.865829	32
114	checkpoint_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:push_filepad	NaN	2020-10-13 23:31:57.814026	2020-10-13 23:31:58.865822	32
115	mp4_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808469	2020-10-13 23:31:58.860104	15
116	surfactant_tail_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808467	2020-10-13 23:31:58.860101	15
117	surfactant_head_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808464	2020-10-13 23:31:58.860099	15
118	substrate_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808462	2020-10-13 23:31:58.860097	15
119	counterion_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808460	2020-10-13 23:31:58.860095	15
120	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808458	2020-10-13 23:31:58.860092	15
121	surfactant_head_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808455	2020-10-13 23:31:58.860090	15
122	surfactant_head_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808453	2020-10-13 23:31:58.860088	15
123	substrate_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808451	2020-10-13 23:31:58.860086	15
124	substrate_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808449	2020-10-13 23:31:58.860084	15
125	counterion_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808446	2020-10-13 23:31:58.860081	15
126	counterion_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808444	2020-10-13 23:31:58.860079	15
127	counterion_substrate_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808442	2020-10-13 23:31:58.860076	15
128	counterion_counterion_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808440	2020-10-13 23:31:58.860074	15
129	run_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808438	2020-10-13 23:31:58.860072	15
130	index_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808435	2020-10-13 23:31:58.860070	15
131	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808433	2020-10-13 23:31:58.860067	15
132	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808431	2020-10-13 23:31:58.860065	15
133	trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808429	2020-10-13 23:31:58.860063	15
134	energy_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808425	2020-10-13 23:31:58.860060	15
135	log_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.808419	2020-10-13 23:31:58.860054	15
136	mp4_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803269	2020-10-13 23:31:58.855226	17
137	surfactant_tail_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803267	2020-10-13 23:31:58.855224	17
138	surfactant_head_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803264	2020-10-13 23:31:58.855222	17
139	substrate_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803262	2020-10-13 23:31:58.855219	17
140	counterion_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803260	2020-10-13 23:31:58.855217	17
141	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803258	2020-10-13 23:31:58.855215	17
142	surfactant_head_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803256	2020-10-13 23:31:58.855213	17
143	surfactant_head_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803253	2020-10-13 23:31:58.855211	17
144	substrate_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803251	2020-10-13 23:31:58.855208	17
145	substrate_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803249	2020-10-13 23:31:58.855206	17
146	counterion_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803247	2020-10-13 23:31:58.855204	17
147	counterion_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803244	2020-10-13 23:31:58.855202	17
148	counterion_substrate_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803242	2020-10-13 23:31:58.855199	17
149	counterion_counterion_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803240	2020-10-13 23:31:58.855197	17
150	run_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803238	2020-10-13 23:31:58.855195	17
151	index_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803235	2020-10-13 23:31:58.855193	17
152	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803233	2020-10-13 23:31:58.855190	17
153	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803231	2020-10-13 23:31:58.855188	17
154	trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803228	2020-10-13 23:31:58.855186	17
155	energy_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803226	2020-10-13 23:31:58.855183	17
156	log_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:push_filepad	NaN	2020-10-13 23:31:57.803220	2020-10-13 23:31:58.855177	17
157	mp4_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798517	2020-10-13 23:31:58.850377	21
158	surfactant_tail_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798515	2020-10-13 23:31:58.850375	21
159	surfactant_head_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798513	2020-10-13 23:31:58.850373	21
160	substrate_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798510	2020-10-13 23:31:58.850371	21
161	counterion_rmsd	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798508	2020-10-13 23:31:58.850369	21
162	surfactant_tail_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798506	2020-10-13 23:31:58.850366	21
163	surfactant_head_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798504	2020-10-13 23:31:58.850364	22
164	surfactant_head_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798501	2020-10-13 23:31:58.850362	22
165	substrate_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798499	2020-10-13 23:31:58.850360	22
166	substrate_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798497	2020-10-13 23:31:58.850358	22
167	counterion_surfactant_tail_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798495	2020-10-13 23:31:58.850355	22
168	counterion_surfactant_head_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798492	2020-10-13 23:31:58.850353	22
169	counterion_substrate_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798490	2020-10-13 23:31:58.850351	22
170	counterion_counterion_rdf	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798488	2020-10-13 23:31:58.850349	22
171	trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798486	2020-10-13 23:31:58.850347	22
172	run_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798483	2020-10-13 23:31:58.850344	23
173	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798481	2020-10-13 23:31:58.850342	23
174	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798479	2020-10-13 23:31:58.850340	23
175	uncompressed_trajectory_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798476	2020-10-13 23:31:58.850337	23
176	energy_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798473	2020-10-13 23:31:58.850334	23
177	log_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:push_filepad	NaN	2020-10-13 23:31:57.798467	2020-10-13 23:31:58.850328	23
178	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad	NaN	2020-10-13 23:31:57.793541	2020-10-13 23:31:58.844403	24
179	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsSolvate:push_filepad	NaN	2020-10-13 23:31:57.793538	2020-10-13 23:31:58.844395	24
180	topology_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad	NaN	2020-10-13 23:31:57.793403	2020-10-13 23:31:58.844100	24
181	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:push_filepad	NaN	2020-10-13 23:31:57.793400	2020-10-13 23:31:58.844092	24
182	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:PDBCleanup:push_filepad	NaN	2020-10-13 23:31:57.793073	2020-10-13 23:31:58.843344	24
183	data_file	SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_filepad	NaN	2020-10-13 23:31:57.792866	2020-10-13 23:31:58.842868	24
184	png_file	SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad	NaN	2020-10-13 23:31:57.792501	2020-10-13 23:31:57.792501	1
185	surfactant_file	SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:push_filepad	NaN	2020-10-13 23:31:57.792495	2020-10-13 23:31:57.792495	1
186	data_file	SubstratePassivation:ComponentMeasures:SubstratePreparation:FormatConversion:push_filepad	NaN	2020-10-13 23:31:57.716886	2020-10-13 23:31:57.716886	1
187	surfactant_file	SubstratePassivation:ComponentMeasures:SurfactantMoleculeMeasures:SurfactantMoleculeMeasuresMain:push_infiles	1_CTAB.pdb	None	None	1
188	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsRelaxation:GromacsRelaxationMain:push_infiles	relax_z_only.mdp	None	None	1
189	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsPrep:GromacsPrepMain:push_infiles	sys.top.template	None	None	1
190	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsTrajectoryVisualization:push_infiles	view.pml.template	None	None	1
191	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNVTEquilibration:GromacsNVTEquilibrationMain:push_infiles	nvt.mdp	None	None	1
192	template	SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles	flat.inp.template	None	None	1
193	counterion_file	SubstratePassivation:BilayerPackingAndEquilibartion:BilayerPacking:LayeredPackingMain:push_infiles	1_BR.pdb	None	None	1
194	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsEnergyMinimizationAfterSolvation:GromacsEnergyMinimizationAfterSolvationMain:push_infiles	em_solvated.mdp	None	None	1
195	input	SubstratePassivation:BilayerPackingAndEquilibartion:GromacsMinimizationEquilibrationRelaxation:GromacsNPTEquilibration:GromacsNPTEquilibrationMain:push_infiles	npt_z_only.mdp	None	None	1

	type	name	earliest	latest	object_count
0	mp4_file	NaN	2020-10-13 23:31:57.798517	2020-10-13 23:31:58.871696	44
1	surfactant_tail_rmsd	NaN	2020-10-13 23:31:57.798515	2020-10-13 23:31:58.871693	44
2	surfactant_head_rmsd	NaN	2020-10-13 23:31:57.798513	2020-10-13 23:31:58.871691	44
3	substrate_rmsd	NaN	2020-10-13 23:31:57.798510	2020-10-13 23:31:58.871689	44
4	counterion_rmsd	NaN	2020-10-13 23:31:57.798508	2020-10-13 23:31:58.871687	44
5	surfactant_tail_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.798506	2020-10-13 23:31:58.871685	44
6	surfactant_head_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.798504	2020-10-13 23:31:58.871682	45
7	surfactant_head_surfactant_head_rdf	NaN	2020-10-13 23:31:57.798501	2020-10-13 23:31:58.871680	45
8	substrate_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.798499	2020-10-13 23:31:58.871678	45
9	substrate_surfactant_head_rdf	NaN	2020-10-13 23:31:57.798497	2020-10-13 23:31:58.871676	45
10	counterion_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.798495	2020-10-13 23:31:58.871674	45
11	counterion_surfactant_head_rdf	NaN	2020-10-13 23:31:57.798492	2020-10-13 23:31:58.871671	45
12	counterion_substrate_rdf	NaN	2020-10-13 23:31:57.798490	2020-10-13 23:31:58.871669	45
13	counterion_counterion_rdf	NaN	2020-10-13 23:31:57.798488	2020-10-13 23:31:58.871667	45
14	trajectory_file	NaN	2020-10-13 23:31:57.798486	2020-10-13 23:31:58.871665	45
15	run_file	NaN	2020-10-13 23:31:57.798483	2020-10-13 23:31:58.871663	46
16	topology_file	NaN	2020-10-13 23:31:57.798481	2020-10-13 23:31:58.871660	46
17	data_file	NaN	2020-10-13 23:31:57.798479	2020-10-13 23:31:58.871658	46
18	uncompressed_trajectory_file	NaN	2020-10-13 23:31:57.798476	2020-10-13 23:31:58.871656	46
19	energy_file	NaN	2020-10-13 23:31:57.798473	2020-10-13 23:31:58.871653	46
20	log_file	NaN	2020-10-13 23:31:57.798467	2020-10-13 23:31:58.871647	46
21	input	view.pml.template	None	None	1
22	input	em_solvated.mdp	None	None	1

	type	name	earliest	latest	object_count
0	mp4_file	NaN	2020-10-13 23:31:57.803269	2020-10-13 23:31:58.855226	30
1	surfactant_tail_rmsd	NaN	2020-10-13 23:31:57.803267	2020-10-13 23:31:58.855224	30
2	surfactant_head_rmsd	NaN	2020-10-13 23:31:57.803264	2020-10-13 23:31:58.855222	30
3	substrate_rmsd	NaN	2020-10-13 23:31:57.803262	2020-10-13 23:31:58.855219	30
4	counterion_rmsd	NaN	2020-10-13 23:31:57.803260	2020-10-13 23:31:58.855217	30
5	surfactant_tail_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.803258	2020-10-13 23:31:58.855215	30
6	surfactant_head_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.803256	2020-10-13 23:31:58.855213	30
7	surfactant_head_surfactant_head_rdf	NaN	2020-10-13 23:31:57.803253	2020-10-13 23:31:58.855211	30
8	substrate_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.803251	2020-10-13 23:31:58.855208	30
9	substrate_surfactant_head_rdf	NaN	2020-10-13 23:31:57.803249	2020-10-13 23:31:58.855206	30
10	counterion_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.803247	2020-10-13 23:31:58.855204	30
11	counterion_surfactant_head_rdf	NaN	2020-10-13 23:31:57.803244	2020-10-13 23:31:58.855202	30
12	counterion_substrate_rdf	NaN	2020-10-13 23:31:57.803242	2020-10-13 23:31:58.855199	30
13	counterion_counterion_rdf	NaN	2020-10-13 23:31:57.803240	2020-10-13 23:31:58.855197	30
14	run_file	NaN	2020-10-13 23:31:57.803238	2020-10-13 23:31:58.855195	30
15	index_file	NaN	2020-10-13 23:31:57.803235	2020-10-13 23:31:58.855193	30
16	topology_file	NaN	2020-10-13 23:31:57.803233	2020-10-13 23:31:58.855190	30
17	data_file	NaN	2020-10-13 23:31:57.803231	2020-10-13 23:31:58.855188	30
18	trajectory_file	NaN	2020-10-13 23:31:57.803228	2020-10-13 23:31:58.855186	30
19	energy_file	NaN	2020-10-13 23:31:57.803226	2020-10-13 23:31:58.855183	30
20	log_file	NaN	2020-10-13 23:31:57.803220	2020-10-13 23:31:58.855177	30
21	input	nvt.mdp	None	None	1

	type	name	earliest	latest	object_count
0	mp4_file	NaN	2020-10-13 23:31:57.808469	2020-10-13 23:31:58.860104	27
1	surfactant_tail_rmsd	NaN	2020-10-13 23:31:57.808467	2020-10-13 23:31:58.860101	27
2	surfactant_head_rmsd	NaN	2020-10-13 23:31:57.808464	2020-10-13 23:31:58.860099	27
3	substrate_rmsd	NaN	2020-10-13 23:31:57.808462	2020-10-13 23:31:58.860097	27
4	counterion_rmsd	NaN	2020-10-13 23:31:57.808460	2020-10-13 23:31:58.860095	27
5	surfactant_tail_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.808458	2020-10-13 23:31:58.860092	27
6	surfactant_head_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.808455	2020-10-13 23:31:58.860090	27
7	surfactant_head_surfactant_head_rdf	NaN	2020-10-13 23:31:57.808453	2020-10-13 23:31:58.860088	27
8	substrate_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.808451	2020-10-13 23:31:58.860086	27
9	substrate_surfactant_head_rdf	NaN	2020-10-13 23:31:57.808449	2020-10-13 23:31:58.860084	27
10	counterion_surfactant_tail_rdf	NaN	2020-10-13 23:31:57.808446	2020-10-13 23:31:58.860081	27
11	counterion_surfactant_head_rdf	NaN	2020-10-13 23:31:57.808444	2020-10-13 23:31:58.860079	27
12	counterion_substrate_rdf	NaN	2020-10-13 23:31:57.808442	2020-10-13 23:31:58.860076	27
13	counterion_counterion_rdf	NaN	2020-10-13 23:31:57.808440	2020-10-13 23:31:58.860074	27
14	run_file	NaN	2020-10-13 23:31:57.808438	2020-10-13 23:31:58.860072	27
15	index_file	NaN	2020-10-13 23:31:57.808435	2020-10-13 23:31:58.860070	27
16	topology_file	NaN	2020-10-13 23:31:57.808433	2020-10-13 23:31:58.860067	27
17	data_file	NaN	2020-10-13 23:31:57.808431	2020-10-13 23:31:58.860065	27
18	trajectory_file	NaN	2020-10-13 23:31:57.808429	2020-10-13 23:31:58.860063	27
19	energy_file	NaN	2020-10-13 23:31:57.808425	2020-10-13 23:31:58.860060	27
20	log_file	NaN	2020-10-13 23:31:57.808419	2020-10-13 23:31:58.860054	27

	nmolecules	name	earliest	latest	object_count
0	1944	NaN	2020-10-13 23:31:58.850377	2020-10-13 23:31:58.871696	2
1	1863	NaN	2020-10-13 23:31:58.806421	2020-10-13 23:31:58.827543	2
2	1782	NaN	2020-10-13 23:31:58.785597	2020-10-13 23:31:58.785597	1
3	1701	NaN	2020-10-13 23:31:58.659185	2020-10-13 23:31:58.736016	2
4	1620	NaN	2020-10-13 23:31:58.636198	2020-10-13 23:31:58.636198	1
5	1539	NaN	2020-10-13 23:31:58.594170	2020-10-13 23:31:58.594170	1
6	1458	NaN	2020-10-13 23:31:58.529462	2020-10-13 23:31:58.529462	1
7	1377	NaN	2020-10-13 23:31:58.486650	2020-10-13 23:31:58.507798	2
8	1296	NaN	2020-10-13 23:31:58.444974	2020-10-13 23:31:58.466124	2
9	1215	NaN	2020-10-13 23:31:58.400662	2020-10-13 23:31:58.421435	2
10	1134	NaN	2020-10-13 23:31:58.357968	2020-10-13 23:31:58.378932	2
11	1053	NaN	2020-10-13 23:31:58.312030	2020-10-13 23:31:58.332801	2
12	972	NaN	2020-10-13 23:31:58.270321	2020-10-13 23:31:58.291287	2
13	891	NaN	2020-10-13 23:31:58.226158	2020-10-13 23:31:58.248728	2
14	810	NaN	2020-10-13 23:31:58.184143	2020-10-13 23:31:58.205036	2
15	729	NaN	2020-10-13 23:31:58.141455	2020-10-13 23:31:58.163404	2
16	648	NaN	2020-10-13 23:31:58.098172	2020-10-13 23:31:58.119601	2
17	567	NaN	2020-10-13 23:31:58.056085	2020-10-13 23:31:58.076899	2
18	486	NaN	2020-10-13 23:31:58.013506	2020-10-13 23:31:58.035070	2
19	405	NaN	2020-10-13 23:31:57.970518	2020-10-13 23:31:57.992373	2
20	324	NaN	2020-10-13 23:31:57.927512	2020-10-13 23:31:57.949348	2
21	243	NaN	2020-10-13 23:31:57.885000	2020-10-13 23:31:57.906330	2
22	162	NaN	2020-10-13 23:31:57.843254	2020-10-13 23:31:57.864389	2
23	81	NaN	2020-10-13 23:31:57.798517	2020-10-13 23:31:57.819837	2

			Time	Bond	U-B	Proper Dih.	LJ-14	Coulomb-14	LJ (SR)	Coulomb (SR)	...	Coul-SR:rest-rest	LJ-SR:rest-rest	Coul-14:rest-rest	LJ-14:rest-rest	T-non-Substrate	T-Substrate	Lamb-non-Substrate	Lamb-Substrate
nmolecules	shape	step
405	bilayer	0.0	0.0	336.762299	5609.709473	15275.146484	-938.929871	-4.498196e+05	-79815064.0	-12370052.0	...	-12550173.0	1.441314e+06	0.0	0.0	299.153046	0.0	1.0	1.0
		1.0	1.0	5569.974609	40000.382812	20775.585938	-77.371773	-4.500497e+05	-80003904.0	-10990010.0	...	-11167832.0	1.273080e+06	0.0	0.0	205.595612	0.0	1.0	1.0
		2.0	2.0	6615.566406	46112.875000	21897.025391	148.110474	-4.500002e+05	-80063808.0	-10682512.0	...	-10852491.0	1.223366e+06	0.0	0.0	237.888718	0.0	1.0	1.0
		3.0	3.0	7130.301758	50295.371094	22627.021484	302.290680	-4.501067e+05	-80122520.0	-10447955.0	...	-10619445.0	1.171972e+06	0.0	0.0	256.536438	0.0	1.0	1.0
		4.0	4.0	7601.223633	53907.386719	22971.468750	399.675079	-4.504439e+05	-80170184.0	-10269777.0	...	-10443889.0	1.129002e+06	0.0	0.0	267.331085	0.0	1.0	1.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
1296	bilayer	96.0	96.0	26367.396484	191188.453125	78572.117188	2578.112793	-1.441748e+06	-80406624.0	-8529983.0	...	-9151689.0	9.921227e+05	0.0	0.0	298.348053	0.0	1.0	1.0
		97.0	97.0	25973.251953	191302.937500	78590.515625	2640.567139	-1.441809e+06	-80405984.0	-8527396.0	...	-9147254.0	9.903748e+05	0.0	0.0	297.865540	0.0	1.0	1.0
		98.0	98.0	26293.732422	190148.890625	78993.523438	2589.545166	-1.441626e+06	-80409384.0	-8529375.0	...	-9149565.0	9.883881e+05	0.0	0.0	298.765686	0.0	1.0	1.0
		99.0	99.0	26275.277344	190356.203125	78729.914062	2658.798096	-1.441912e+06	-80411120.0	-8522873.0	...	-9144062.0	9.875896e+05	0.0	0.0	298.079498	0.0	1.0	1.0
		100.0	100.0	26459.773438	191251.671875	78547.992188	2645.103271	-1.441487e+06	-80403800.0	-8533594.0	...	-9154591.0	9.926151e+05	0.0	0.0	298.365936	0.0	1.0	1.0

			Time	Bond	U-B	Proper Dih.	LJ-14	Coulomb-14	LJ (SR)	Coulomb (SR)	...	Coul-SR:rest-rest	LJ-SR:rest-rest	Coul-14:rest-rest	LJ-14:rest-rest	T-non-Substrate	T-Substrate	Lamb-non-Substrate	Lamb-Substrate
shape	nmolecules	step
bilayer	1944	0.0	0.0	39936.410156	289935.437500	118923.296875	3601.251709	-2.160646e+06	-84339680.0	-7723825.0	...	-8765402.0	9.768656e+05	0.0	0.0	296.816742	2.699537	1.0	1.0
		1.0	1.0	39717.855469	286455.187500	122287.273438	3941.893066	-2.157035e+06	-84362672.0	-7709268.0	...	-8746435.0	9.679704e+05	0.0	0.0	298.772247	3.253741	1.0	1.0
		2.0	2.0	39786.585938	282673.281250	121678.007812	4082.935791	-2.155238e+06	-84353024.0	-7711732.0	...	-8742852.0	9.703966e+05	0.0	0.0	298.515228	3.192918	1.0	1.0
		3.0	3.0	39369.175781	280971.593750	122375.289062	4018.603760	-2.151787e+06	-84352016.0	-7717448.5	...	-8744444.0	9.695025e+05	0.0	0.0	297.532349	3.061393	1.0	1.0
		4.0	4.0	39469.574219	280759.625000	121373.687500	3896.191895	-2.150179e+06	-84369072.0	-7709955.0	...	-8732732.0	9.560571e+05	0.0	0.0	297.537567	3.020302	1.0	1.0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
cylinders	729	2996.0	2996.0	13508.846680	93825.765625	42622.656250	470.645233	-7.913297e+05	-84183760.0	-9476877.0	...	-9773378.0	1.037954e+06	0.0	0.0	295.217285	2.965389	1.0	1.0
		2997.0	2997.0	13331.565430	93072.046875	42518.507812	456.470490	-7.912239e+05	-84179056.0	-9484637.0	...	-9780930.0	1.042440e+06	0.0	0.0	295.269592	2.979168	1.0	1.0
		2998.0	2998.0	13445.263672	93784.937500	42998.128906	444.005981	-7.910263e+05	-84184760.0	-9476664.0	...	-9773029.0	1.036592e+06	0.0	0.0	294.636444	2.977165	1.0	1.0
		2999.0	2999.0	13504.045898	93202.882812	42822.843750	448.560028	-7.914327e+05	-84181440.0	-9472594.0	...	-9769012.0	1.038523e+06	0.0	0.0	294.838196	2.954648	1.0	1.0
		3000.0	3000.0	13544.460938	93906.226562	42708.632812	456.516785	-7.915608e+05	-84181992.0	-9472383.0	...	-9770683.0	1.039171e+06	0.0	0.0	294.818451	2.965106	1.0	1.0